Did Kaepernick really call 49ers a ‘phenomenal organization’?

Colin Kaepernick didn’t just kneel on the 49ers sideline in San Diego.

He high-fived last-stringers, offensive and defensive players alike. He watched with glee as a fourth-quarter comeback capped the 49ers’ exhibition season. He acted like a happy teammate, no matter how unhappy he is with America’s social issues and rogue police.

Amid Kaepernick’s post-game discourse about sociological ideals – he’s pledging $1 million and his time to unnamed community ventures – he also talked about his growing bond with a team, a franchise, he nearly ditched four months ago.

“This is a phenomenal organization,” Kaepernick said. “I’ve had great conversations here. I’ve had great memories here.”

“This team has given me the opportunity to become the man I am today,” Kaepernick continued. “And I’m grateful for that. I’m thankful for that. And San Francisco has become my home.”

Not all memories have been great. Distrust with the front office — over leaks about his persona, over financial and medical issues — led Kaepernick to pursue a trade and nearly call Denver home in April. As recently as Sunday, he had to win back teammates by explaining his quest for harmony across America and justice to oppressed countrymen.

Yes, he’s still a Niner, presuming Thursday’s first-half performance convinced the 49ers to keep him – and his equal-rights campaign – on the roster through Saturday’s cuts.

Coach Chip Kelly wouldn’t discuss Kaepernick’s roster plight post-game, other than to say film would be evaluated and all personnel calls are up to general manager Trent Baalke. While Kelly publicly kept any praise of in check, he did high-five Kaepernick as he got on the bus for the airport, safety Eric Reid told the Dan Patrick Show on Friday morning.

Even if, as expected, Kaepernick doesn’t overtake Blaine Gabbert for the Sept. 12, season-opening starting job, Kaepernick seems OK with it. He is, after all, moonlighting as the quarterback for a social movement under the spotlight afforded to America’s most popular sport.

“I don’t think it’s a distraction at all,” Kaepernick said. “It’s really brought our team closer, because we got closer to each other on a personal level, so we understand each other better.

“We go out on the field, we fight for each other, because we know we’re fighting for the same thing.”

Are his teammates buying that? Some are. Reid certainly is, having talked extensively with Kaepernick before deciding to kneel next to him during their national-anthem protest in San Diego.

“I talked to Colin and right now his goal is to keep the dialogue open,” Reid said. “He believes that nothing is going to change unless it’s talked about first, but then ultimately to get into the community and start affecting change on those issues.”

Reid said he and Kaepernick talked for multiple days about making sure that message isn’t lost amid an anthem protest, which they hoped to accomplish by kneeling rather than sitting. That tactic was hatched during a visit earlier in the day with Nate Boyer, a Green Beret who auditioned with the 49ers as a long snapper last year; Boyer stood at Kaepernick’s side during Thursday’s pregame ceremony.

“(Kaepernick) saw that it hurt people that he sat during the national anthem,” Reid added. “There are people that actually put their lives on the line for this country to give us freedom.”

The people Kaepernick played with Thursday night were all backups. Yet somehow an exhibition finale seemed to pack as much pressure as Super Bowl XLVII for Kaepernick. That was four seasons ago, when he broke out as the franchise’s new star.

Now, he’s an embattled veteran who’s civic dreams are reconnecting him with fellow 49ers, or so he believes.

“I’ve had conversations with people They really do understand what I’m trying to do, and who I’m trying to help. That’s huge,” Kaepernick said. “Understanding each other is a big step toward treating each other the right way.”

Kaepernick hasn’t publicly had any problem with his teammates or new coaches. But one mention of the police and he lets loose. He’s repeatedly riffed about “rogue” cops endangering ones like his uncles and friends who “genuinely want to help and protect people.”

“We have cops that are murdering people. We have cops in SFPD that are blatantly racist,” Kaepernick said. “Those issues need to be addressed.”

Kaepernick’s protest is rubbing off on more than Reid. Seattle Seahawks cornerback Jeremy Lane sat through the national anthem at his game against the Raiders. Denver Broncos offensive tackle Russell Okung, writing for The Players Tribune, pledged his support for Kaepernick and his cause: “We see you, man. Thank you for reigniting the conversation and the movement for change.”

Kaepernick said he’s willing to take up the SFPD’s offer of visiting its academy. He’s working with unnamed organizations to help communities. And he’s still got a day job of playing for the 49ers.

— Kelly said the 49ers won’t pare their roster to the 53-man limit until Saturday’s 1 p.m. deadline, after which he’ll talk with the media on a conference call.

— Linebacker Michael Wilhoite, a starter the past two seasons, played all four quarters and made six tackles while missing a couple. Gerald Hodges and Ray-Ray Armstrong, who were competing with Wilhoite for the weak-side linebacker role, did not suit up.

— Marcus Rush’s two sacks Thursday gave him six for the exhibition season. He also had an interception off a pass deflected by Rashard Robinson, who had an interception himself.

— Mike Davis ran for a team-high 148 yards (7.8 yards per carry) in the exhibition season, followed by DuJuan Harris (131; 4.7) and Kelvin Taylor (107; 5.1). Davis also led the 49ers with seven receptions.